Aims

The STRENDA project focuses on three main aims: The establishment of publication standards for enzyme activity data, the standardization of assay conditions and the development of an electronic submission system for enzyme data (STRENDA DB).

 

 

 

1. Publication standards

The STRENDA Commission establishes standards of reporting enzyme data to allow a full understanding of the conditions under which they were obtained. The aim is that such standards will become adopted by the major scientific journals and databases, such as BRENDA and SABIO-RK that compile enzyme activity and kinetic data.

 

Status

The STRENDA Commission has drawn up two guideline lists: List Level 1A defines the data that are required for a complete description of the materials and methods which were used in the experiments. List Level 1B defines the parameters to describe the enzyme activity data. Both lists are accessible under Guidelines.

Currently more than 30 international biochemistry journals recommend the STRENDA guidelines.

(June 2014)

The following journals recommend authors to consider the guidelines when reporting enzymology data:

  • Archives in Biochemistry and Biophysics
  • Biochimica et Biophysica Acta (alle nine sections)
  • Biochemical and Biophysical Research Communications
  • Biochemistry
  • FEBS Journal
  • Nature Chemical Biology
  • The Journal of Biological Chemistry
  • ACS Catalysis
  • Antimicrobial Agents and Chemotherapy
  • Biochemical Journal
  • Clinical and Vaccine Immunology
  • Free Radical Research
  • Infection and Immunity
  • Journal of the American Chemical Society
  • mBio
  • Molecular and Cellular Biology
  • Proceedings of the National Academy of Sciences
  • The Journal of Bacteriology
  • The Journal of Virology
  • Trends in Biotechnology

The nine sections of Biochimica et Biophysica Acta are:

  • BBA - Bioenergetics
  • BBA - Biomembranes
  • BBA - Gene Regulatory Mechanisms
  • BBA - General Subjects
  • BBA - Molecular Basis of Disease
  • BBA - Molecular Cell Research
  • BBA - Molecular and Cell Biology of Lipids
  • BBA - Proteins and Proteomics
  • BBA - Reviews on Cancer

Since 2008, the STRENDA guidelines have been included in the MIBBI portal. MIBBI, as part of the BioSharing project stands for “Minimum Information for Biological and Biomedical Investigations”. It is a project that provides the community a portal for 'minimum information' checklists to support authors, reviewers and editors in order to improve the quality of the published scientific data. The following publishers and journals recommend the authors to use the normative checklists from the MIBBI portal when publishing their research results.


Publishers

  • BioMedCentral (z. B. BMC Bioinformatics, BMC Biochemistry, BMC Biology, BMC Systems Biology, ...)
  • PLoS (z. B. PLoS One, PLoS Biology, PLoS Medicine, ...)


Journals

  • OMICS

(June 2014)

 

2. Standardization of assay conditions

A second goal of the STRENDA Commission is to derive uniform assay standards for the standardization of data for single enzymes and groups of enzymes. The conditions under which an enzyme operates depend on the organism and organelle in which it occurs. For example, the physiological temperature at which an enzyme operates in a mammal may have little relevance to the behavior of the corresponding enzyme in a hyperthermophile. On the other hand, using very different assay conditions for assaying the forward and reverse reactions catalyzed by the same enzyme may mean that valuable thermodynamic data are lost.


The basis of initial assay standards can be the physiological conditions, which are those conditions in which cells, tissues, organs, or even the whole organism are present. However, these conditions first need to be determined.

Status

First attempts towards the standardization of the assay conditions were made when compiling List Level 2. This list is still in a rudimentary state and currently subject of intense discussions within the Commission.

In collaboration with a number of Dutch working groups, a standard assay for the enzymes from the glycolysis of baker's yeast has been defined and tested resulting in obtaining the essential kinetics of all enzymes involved in this pathway. This approach can be regarded a proof-of-principle which can be applied with modifications for the characterization of additional metabolic pathways (van Eunen et al. (2010) FEBS J. 277(3):749-760).

(June 2014)

3. STRENDA DB: The development of an electronic submission system for enzyme data

The STRENDA guidelines were developed through extensive interactions with the biochemical community and are currently recommended by more than 30 biochemistry journals. The electronic data-submission system (STRENDA DB) incorporates these guidelines in a web-based portal for the submission of data to a freely accessible, public database. The aim is to develop a submission system for enzyme data that can be integrated into the publication practices of the community.

Authors will be requested to enter the experimental data from their manuscript into an input mask. During this input process the data is automatically checked for its compliance with the STRENDA guidelines. The author receives a registration number as proof of compliance with the STRENDA guidelines after completion of the entry and successful validation of the data. It is noteworthy that the data is validated only with regards to formal completeness. The submission system does not check the quality of the data which is up to the reviewers of the respective journal.

The data is stored in the database and made accessible to the public as soon as the manuscript data are reviewed and published in a journal.

The objectives of STRENDA DB are:

  • Validation of the data in compliance with the STRENDA guidelines;
  • Building an enzyme kinetics database, in which the kinetics data are stored along with the assay conditions.

Status

The prototype of STRENDA DB was presented to the public at a number of conferences. The positive responses of the community encouraged the STRENDA Commission to develop a first version of STRENDA DB lead-managed by the Beilstein-Institut. This version combines a controlled data submission system for enzyme kinetic data with the generation of a database.

A prototype of STRENDA DB was presented to the public at a number of conferences. The positive responses of the community encouraged the STRENDA Commission to develop a first version of STRENDA DB lead-managed by the Beilstein-Institut. This version combines a controlled data submission system for enzyme kinetic data with the generation of a database.

Today, STRENDA DB is in the beta testing phase. It is planned to release the first version of STRENDA DB in 2015. Before this release, interested scientists can have a look at the current release candidate version 0.91 of STRENDA DB.

(May 2015)